There are several intertwined issues here.
Human rights of the Pre-Cogs
The Pre-Crime system depends in a crucial way on the constant participation of the Pre-Cogs, held in a (not necessarily pleasant) state that maximizes their perceptive abilities. While the film does not emphasize directly the issue of their rights, by the end it is clear that they are individuals who value an ordinary life and privacy.
Pre-Crime is not always right
The ending of the film proves that Pre-Crime cannot always predict an outcome correctly. Anderton explains that if Burgess kills him, then the Pre-Crime prediction will be vindicated. If he decides not to kill Anderton, then Pre-Crime will be shown to be faulty. This shows us the inherent flaw of Pre-Crime: when the future is made known to people, they have the power to change it. Indeed, Burgess shoots himself.
Although halo-ing is part of the problem, it is not the main problem. The problem is that Pre-Crime cannot always predict the future with certainty. You can argue that they can take steps to investigate a Pre-Crime report without halo-ing, but any punishment taken will result in a loss of rights for a possibly innocent person — unless of course no punishment is enforced at all and all that is sought is prevention. This requires a complete rethink of what it means to achieve justice.
But we still have the first issue. Even if prevention is enough, the system itself requires the loss of liberty — essentially enslavement and constant sensory deprivation — for the Pre-Cogs, who have expressed a preference for a solitary but normal life by the film's conclusion.
Its founder is a murderer!
You might argue that this is a society that did not care about Pre-Cog rights before, so why would they care now? Clearly something has changed in the public's mind, as there are no demands from the public to reinstate the Pre-Cogs and continue the program.
We can't rule out the influence of bad press. The fact that Pre-Crime's founder, Lamar Burgess, turned out to be a murderer himself is the kind of scandal that could certainly destroy the public's confidence in Pre-Crime, at least for a few years.
Apparently this (bad press / poor public opinion) is precisely the reason why the Pre-Cog-based Pre-Crime program was abandoned, according to the television continuation, in which a computerized version of Pre-Crime is created. The series also focuses on the human rights of the Pre-Cogs. (Thanks to Izkata and T.J.L. for pointing this out.)